Small-scale fisheries supplying tropical sea cucumbers to Asian markets frequently overharvest stocks, incurring unknown loss of economic value. An indication of such value loss can provide economic incentives for better conservation and management. However, “before and after” time-series by which loss could be calculated are generally not available for most sea cucumber fisheries. In this study we provide a snapshot comparison of stocks of three characteristic sea cucumber species in two islands in the Western Indian Ocean: Zanzibar (open-access fishery) and Mayotte (stocks protected since 2004). Our aim is to provide an indication of reference economic value of holothurian populations under two contrasting management regimes. Comparisons were made from stock appraisals using transects, linked to the species-specific market value, and compared between similar habitats from both locations. Surveyed habitats in Mayotte held sea cucumber stocks with a mean economic value of USD556.90 ± 110.30/ha, compared with USD1.73 ± 0.58/ ha in Zanzibar. A 5% harvest of sea cucumbers from surveyed areas in Mayotte would yield about 20 times greater income than harvesting the total surveyed stock in Zanzibar. By illustrating the economic value when strong management measures are implemented, this study highlights existing economic values and shows that sea cucumber fisheries in the tropics are a resource worth investing in and with high potential for social-economic benefits if properly managed.